Selenium (Se)-enriched broccoli has health-beneficial selenium-containing compounds, but it may contain reduced amounts of chemopreventive glucosinolates. To investigate the basis by which Se treatment influences glucosinolate levels, we treated two broccoli cultivars with 25 μM Na2SeO4. We found that Se supplementation suppressed the accumulation of total glucosinolates, particularly glucoraphanin, the direct precursor of a potent anticancer compound, in broccoli florets and leaves. We showed that the suppression was not associated with plant sulfur nutrition. The levels of the glucosinolate precursors methionine and phenylalanine as well as the expression of genes involved in glucosinolate biosynthesis were greatly decreased following Se supplementation. Comparative proteomic analysis identified proteins in multiple metabolic and cellular processes that were greatly affected and detected an enzyme affecting methionine biosynthesis that was reduced in the Se-biofortified broccoli. These results indicate that Se-conferred glucosinolate reduction is associated with negative effects on precursor amino acid biosynthesis and glucosinolate-biosynthetic-gene expression and provide information for a better understanding of glucosinolate accumulation in response to Se supplementation in broccoli.